<div dir="ltr"><div class="markdown-here-wrapper" id="markdown-here-wrapper-2522" style><p style="margin:1.2em 0px!important">That worked! Thanks again, Carson.</p>
<p style="margin:1.2em 0px!important">A note for the record: I found that <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">keep_preds=1</code> carries forward <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">pred_gff</code> annotations, but not <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">model_gff</code> annotations when that GFF file uses <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">match</code> and <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">match_part</code> annotations (like a munged GlimmerHMM GFF file), which makes sense I guess now that I think about it.</p>
<p style="margin:1.2em 0px!important">Cheers,<br>Shaun</p>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 10 April 2014 14:35, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>keep_preds=1 will force MAKER to keep ab initio results even if their is no evidence supporting them.</div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<div class=""><span style="font-weight:bold">From: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>><br><span style="font-weight:bold">Reply-To: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>><br>
</div><span style="font-weight:bold">Date: </span> Thursday, April 10, 2014 at 3:32 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] Using GlimmerHMM with MAKER<br></div><div><div class="h5"><div><br></div><div dir="ltr">Thanks, Carson. That helps. I'm trying to do a completely ab initio gene annotation without any est or protein homology evidence, at least for now. The GFF file produce by maker is empty. How do I carry the GlimmerHMM pred_gff (or model_gff) annotations through to the end? Ultimately, I'd like to merge annotations from multiple ab initio predictions.<div>
<br></div><div>Cheers,</div><div>Shaun</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 10 April 2014 11:53, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Make sure it's not GTF or GFF2, but if it is GFF3 You can substitute match for mRNA and match_part for CDS. Then it will be interpreted as a two level alignments feature which can be given to pred_gff.</div>
<div><br></div><div>--Carson</div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>><br><span style="font-weight:bold">Reply-To: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span> Thursday, April 10, 2014 at 12:34 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> [maker-devel] Using GlimmerHMM with MAKER<br></div><div><div><br></div><div dir="ltr">The GlimmerHMM gene prediction software outputs a GFF file that includes mRNA and CDS features, but it does not include gene or exon features, and so it does not appear to be working with MAKER. Has anyone else used GlimmerHMM with MAKER, and how did you deal with this issue?<div>
<br></div><div>Cheers,</div><div>Shaun</div></div></div>
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